Fast-Growth Thermodynamic Integration: Calculating Excess Chemical Potentials of Additive Molecules in Polymer Microstructures

Role of Crystal Disorder and Mechanoactivation in Solid-State Stability of Pharmaceuticals

Common energy-intensive processes applied in oral solid dosage development, such as milling, sieving, blending, compaction, etc. generate particles with surface and bulk crystal disorder. An intriguing aspect of the generated crystal disorder is its evolution and repercussion on the physical- and chemical stabilities of drugs. In this review, we firstly examine the existing literature on crystal disorder and its implications on solid-state stability of pharmaceuticals. Secondly, we discuss the key aspects related to the generation and evolution of crystal disorder, dynamics of the disordered/amorphous phase, analytical techniques to measure/quantify them, and approaches to model the disordering propensity from first principles. The main objective of this compilation is to provide special impetus to predict or model the chemical degradation(s) resulting from processing-induced manifestation in bulk solid manufacturing. Finally, a generic workflow is proposed that can be useful to investigate the relevance of crystal disorder on the degradation of pharmaceuticals during stability studies. The present review will cater to the requirements for developing physically- and chemically stable drugs, thereby enabling early and rational decision-making during candidate screening and in assessing degradation risks associated with formulations and processing.

Modelling Sorption and Transport of Gases in Polymeric Membranes across Different Scales: A Review

Professor Giulio C. Sarti has provided outstanding contributions to the modelling of fluid sorption and transport in polymeric materials, with a special eye on industrial applications such as membrane separation, due to his Chemical Engineering background. He was the co-creator of innovative theories such as the Non-Equilibrium Theory for Glassy Polymers (NET-GP), a flexible tool to estimate the solubility of pure and mixed fluids in a wide range of polymers, and of the Standard Transport Model (STM) for estimating membrane permeability and selectivity. In this review, inspired by his rigorous and original approach to representing membrane fundamentals, we provide an overview of the most significant and up-to-date modeling tools available to estimate the main properties governing polymeric membranes in fluid separation, namely solubility and diffusivity. The paper is not meant to be comprehensive, but it focuses on those contributions that are most relevant or that show the potential to be relevant in the future. We do not restrict our view to the field of macroscopic modelling, which was the main playground of professor Sarti, but also devote our attention to Molecular and Multiscale Hierarchical Modeling. This work proposes a critical evaluation of the different approaches considered, along with their limitations and potentiality.

Atomistic Modeling of Hydrogen and Oxygen Solubility in Semicrystalline PA-6 and HDPE Materials

Hydrogen is a clean and sustainable energy carrier which plays a major role in the transition of the global energy market to a less fossil fuel dependent future. Polymer-based materials are crucial in the production, storage, transportation, and energy extraction of hydrogen. More insights in the hydrogen-polymers interactions are required to guide material design and product development, especially for hydrogen solubility in polymers, which is crucial in many applications. The current study aims at rationalizing the determining factors of hydrogen solubility in two relevant polymers: polyamide-6 (PA-6) and high density polyethylene (HDPE). Based on atomistic molecular dynamics simulations and experimental data, we have reached several conclusions related to hydrogen and oxygen solubility in these two polymers. The crystal phases of PA-6 and HDPE are impenetrable to hydrogen and oxygen at elevated pressures, despite the small molecular size of hydrogen and oxygen. The practical implication for gas barrier applications is that polymer crystals act as impermeable obstacles and gas migration takes place primarily in the amorphous phase. Experimental hydrogen and oxygen solubilities in PA-6 and HDPE at elevated pressures can be predicted in a semiquantitative manner by molecular simulations. The discrepancies between experimental and predicted values could be attributed to neglect of the effect of crystal regions on the amorphous polymer domains. Although hydrogen is smaller than oxygen, it has been experimentally observed that hydrogen has a lower solubility in PA-6 and HDPE than oxygen. This observation has been confirmed by molecular simulations and attributed to the more favorable energetic interactions of oxygen with PA-6 and PE than of hydrogen. These interactions dominate the solubility behavior over the distribution of the accessible volume in the polymers.

Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study

Amorphous solid dispersions are considered a promising formulation strategy for the oral delivery of poorly soluble drugs. The limiting factor for the applicability of this approach is the physical (in)stability of the amorphous phase in solid samples. Minimizing the risk of reduced shelf life for a new drug by establishing a suitable excipient/polymer-type from first principles would be desirable to accelerate formulation development. Here, we perform Molecular Dynamics simulations to determine properties of blends of eight different polymer–small molecule drug combinations for which stability data are available from a consistent set of literature data. We calculate thermodynamic factors (mixing energies) as well as mobilities (diffusion rates and roto-vibrational fluctuations). We find that either of the two factors, mobility and energetics, can determine the relative stability of the amorphous form for a given drug. Which factor is rate limiting depends on physico-chemical properties of the drug and the excipients/polymers. The methods outlined here can be readily employed for an in silico pre-screening of different excipients for a given drug to establish a qualitative ranking of the expected relative stabilities, thereby accelerating and streamlining formulation development.

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg2+ → Ca2+ transformations than traditional linear alchemical pathways (with and without soft-core potentials). The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed (e.g., single call to particle-mesh Ewald) leading to better performance. In the case of AMBER, this enables all the performance benefits of GPU-acceleration to be realized, in addition to unlocking the full spectrum of features available within the MD software, such as Hamiltonian replica exchange (HREM). The TI derivative evaluation can be accomplished efficiently in a post-processing step by reanalyzing the statistically independent trajectory frames in parallel for high throughput. We also show how one can evaluate the particle mesh Ewald contribution to the TI derivative evaluation without needing to perform two reciprocal space calculations. We apply the PI-TI method with HREM on GPUs in AMBER to predict p Ka values in double stranded RNA molecules and make comparison with experiments. Convergence to under 0.25 units for these systems required 100 ns or more of sampling per window and coupling of windows with HREM. We find that MM charges derived from ab initio QM/MM fragment calculations improve the agreement between calculation and experimental results.

Molecular thermodynamics for food science and engineering

We argue that thanks to molecular modeling approaches, many thermodynamic properties required in Food Science and Food Engineering will be calculable within a few hours from first principles in a near future. These new possibilities will enable to bridge via multiscale modeling composition, process and storage effects to reach global optimization, innovative concepts for food or its packaging. An outlook of techniques and a series of examples are given in this perspective. We emphasize solute chemical potentials in polymers, liquids and their mixtures as they cannot be understood and estimated without theory. The presented atomistic and coarse-grained methods offer a natural framework to their conceptualization in polynary systems, entangled or crosslinked homo- or heteropolymers.

Extensive Assessment of Various Computational Methods for Aspartate's pKa Shift

A series of computational methods for pK_a shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pK_a values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pK_a shift being 1.82 pK_a units. The constant pH molecular dynamics (MD), alchemical methods, PROPKA3.1, and multiconformation continuum electrostatics give RMSDs of 1.52, 2.58, 1.37, and 3.52 pK_a units, respectively, on the benchmark set. The empirical scoring method is the most accurate one with extremely low computational cost, and the pH-dependent model is also able to provide accurate results, while the accuracy of MD sampling incorporating alchemical free energy simulation is prohibited by convergence achievement and the performance of conformational search incorporating multiconformation continuum electrostatics is bad. Former research works did not define statistical uncertainty with care and yielded the questionable conclusion that alchemical methods perform well in most benchmarks. In this work the traditional alchemical methods are thoroughly tested for high variants. We also performed the first application of nonequilibrium alchemical methods to the pK_a cases.

Predicting diffusion coefficients of chemicals in and through packaging materials

Most of the physicochemical properties in polymers such as activity and partition coefficients, diffusion coefficients, and their activation with temperature are accessible to direct calculations from first principles. Such predictions are particularly relevant for food packaging as they can be used (1) to demonstrate the compliance or safety of numerous polymer materials and of their constitutive substances (e.g. additives, residues…), when they are used: as containers, coatings, sealants, gaskets, printing inks, etc. (2) or to predict the indirect contamination of food by pollutants (e.g. from recycled polymers, storage ambiance…) (3) or to assess the plasticization of materials in contact by food constituents (e.g. fat matter, aroma…). This review article summarizes the classical and last mechanistic descriptions of diffusion in polymers and discusses the reliability of semi-empirical approaches used for compliance testing both in EU and US. It is concluded that simulation of diffusion in or through polymers is not limited to worst-case assumptions but could also be applied to real cases for risk assessment, designing packaging with low leaching risk or to synthesize plastic additives with low diffusion rates.

Molecular order in a chromonic liquid crystal: a molecular simulation study of the anionic azo dye sunset yellow

We have carried out a detailed atomic simulation study of molecular order within a chromonic liquid crystalline material (sunset yellow) in aqueous solution. Self-assembly occurs in dilute solutions to form stacked aggregates, which show a preference for head-to-tail stacking and antiparallel dipole order. This feature is independent of solution concentration and aggregate size. Stacks are found to be dynamic entities in which rotational transitions (flips) can occur between antiparallel and parallel configurations. At a concentration matching the nematic phase of sunset yellow, the simulations show chromonic columns with a loose hexagonal packing and an intercolumn distance of 2.36 nm. Partial condensation of sodium ions occurs around a chromonic stack, with two preferred binding sites identified for sodium ions, corresponding to strong binding with the oxygens of a sulfonate group and a bridging site between a pair of molecules in a stack. A value for the free energy of binding of a molecule to a stack of 7 k(B)T was obtained for stacks of three and eight molecules, with a slightly larger value (additional 2 kJ mol(-1)) obtained for the dimer binding energy, indicating that aggregation is approximately isodesmic.

Water harvesting using a conducting polymer: a study by molecular dynamics simulation

The results of extensive molecular simulations of adsorption and diffusion of water vapor in polyaniline, made conducting by doping it with HCl or HBr over a broad range of temperatures, are reported. The atomistic model of the polymers was generated using energy minimization, equilibrium molecular dynamics simulations, and two different force fields. The computed sorption isotherms are in excellent agreement with the experimental data. The computed activation energies for the diffusion of water molecules in the polymers also compare well with what has been reported in the literature. The results demonstrate the potential of conducting polyaniline for water harvesting from air.